[AMBER] Restraining the distance between two groups of residues?

From: Gustavo Seabra <gustavo.seabra.gmail.com>
Date: Fri, 8 Oct 2021 14:34:46 -0400

Hi all,

This may be real simple, but I'm having difficulty defining it here. Say I
want to run an MD where the distance between two groups of residues is
restrained. For example, is it possible to restrain the distance between
the COM of residues :1-10 and the COM of residues :90-100?

If so, could that work on pmemd.cuda as well?

I tried using
distance( com(:1-10) com(:90-100) )

but sander complains with "Error: Invalid residue number or atom name in
restraint." and pmemd.cuda refuses to read the "distance" command at all.

(btw, I'm using Amber20)

Gustavo Seabra.
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Received on Fri Oct 08 2021 - 12:00:02 PDT
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